More on Science
Michael Hunter, MD
3 years ago
5 Drugs That May Increase Your Risk of Dementia
While our genes can't be changed easily, you can avoid some dementia risk factors. Today we discuss dementia and five drugs that may increase risk.
Memory loss appears to come with age, but we're not talking about forgetfulness. Sometimes losing your car keys isn't an indication of dementia. Dementia impairs the capacity to think, remember, or make judgments. Dementia hinders daily tasks.
Alzheimers is the most common dementia. Dementia is not normal aging, unlike forgetfulness. Aging increases the risk of Alzheimer's and other dementias. A family history of the illness increases your risk, according to the Mayo Clinic (USA).
Given that our genes are difficult to change (I won't get into epigenetics), what are some avoidable dementia risk factors? Certain drugs may cause cognitive deterioration.
Today we look at four drugs that may cause cognitive decline.
Dementia and benzodiazepines
Benzodiazepine sedatives increase brain GABA levels. Example benzodiazepines:
Diazepam (Valium) (Valium)
Alprazolam (Xanax) (Xanax)
Clonazepam (Klonopin) (Klonopin)
Addiction and overdose are benzodiazepine risks. Yes! These medications don't raise dementia risk.
USC study: Benzodiazepines don't increase dementia risk in older adults.
Benzodiazepines can produce short- and long-term amnesia. This memory loss hinders memory formation. Extreme cases can permanently impair learning and memory. Anterograde amnesia is uncommon.
2. Statins and dementia
Statins reduce cholesterol. They prevent a cholesterol-making chemical. Examples:
Atorvastatin (Lipitor) (Lipitor)
Fluvastatin (Lescol XL) (Lescol XL)
Lovastatin (Altoprev) (Altoprev)
Pitavastatin (Livalo, Zypitamag) (Livalo, Zypitamag)
Pravastatin (Pravachol) (Pravachol)
Rosuvastatin (Crestor, Ezallor) (Crestor, Ezallor)
Simvastatin (Zocor) (Zocor)
This finding is contentious. Harvard's Brigham and Womens Hospital's Dr. Joann Manson says:
“I think that the relationship between statins and cognitive function remains controversial. There’s still not a clear conclusion whether they help to prevent dementia or Alzheimer’s disease, have neutral effects, or increase risk.”
This one's off the dementia list.
3. Dementia and anticholinergic drugs
Anticholinergic drugs treat many conditions, including urine incontinence. Drugs inhibit acetylcholine (a brain chemical that helps send messages between cells). Acetylcholine blockers cause drowsiness, disorientation, and memory loss.
First-generation antihistamines, tricyclic antidepressants, and overactive bladder antimuscarinics are common anticholinergics among the elderly.
Anticholinergic drugs may cause dementia. One study found that taking anticholinergics for three years or more increased the risk of dementia by 1.54 times compared to three months or less. After stopping the medicine, the danger may continue.
4. Drugs for Parkinson's disease and dementia
Cleveland Clinic (USA) on Parkinson's:
Parkinson's disease causes age-related brain degeneration. It causes delayed movements, tremors, and balance issues. Some are inherited, but most are unknown. There are various treatment options, but no cure.
Parkinson's medications can cause memory loss, confusion, delusions, and obsessive behaviors. The drug's effects on dopamine cause these issues.
A 2019 JAMA Internal Medicine study found powerful anticholinergic medications enhance dementia risk.
Those who took anticholinergics had a 1.5 times higher chance of dementia. Individuals taking antidepressants, antipsychotic drugs, anti-Parkinson’s drugs, overactive bladder drugs, and anti-epileptic drugs had the greatest risk of dementia.
Anticholinergic medicines can lessen Parkinson's-related tremors, but they slow cognitive ability. Anticholinergics can cause disorientation and hallucinations in those over 70.
5. Antiepileptic drugs and dementia
The risk of dementia from anti-seizure drugs varies with drugs. Levetiracetam (Keppra) improves Alzheimer's cognition.
One study linked different anti-seizure medications to dementia. Anti-epileptic medicines increased the risk of Alzheimer's disease by 1.15 times in the Finnish sample and 1.3 times in the German population. Depakote, Topamax are drugs.
Sara_Mednick
3 years ago
Since I'm a scientist, I oppose biohacking
Understanding your own energy depletion and restoration is how to truly optimize
Hack has meant many bad things for centuries. In the 1800s, a hack was a meager horse used to transport goods.
Modern usage describes a butcher or ax murderer's cleaver chop. The 1980s programming boom distinguished elegant code from "hacks". Both got you to your goal, but the latter made any programmer cringe and mutter about changing the code. From this emerged the hacker trope, the friendless anti-villain living in a murky hovel lit by the computer monitor, eating junk food and breaking into databases to highlight security system failures or steal hotdog money.
Now, start-a-billion-dollar-business-from-your-garage types have shifted their sights from app development to DIY biology, coining the term "bio-hack". This is a required keyword and meta tag for every fitness-related podcast, book, conference, app, or device.
Bio-hacking involves bypassing your body and mind's security systems to achieve a goal. Many biohackers' initial goals were reasonable, like lowering blood pressure and weight. Encouraged by their own progress, self-determination, and seemingly exquisite control of their biology, they aimed to outsmart aging and death to live 180 to 1000 years (summarized well in this vox.com article).
With this grandiose north star, the hunt for novel supplements and genetic engineering began.
Companies selling do-it-yourself biological manipulations cite lab studies in mice as proof of their safety and success in reversing age-related diseases or promoting longevity in humans (the goal changes depending on whether a company is talking to the federal government or private donors).
The FDA is slower than science, they say. Why not alter your biochemistry by buying pills online, editing your DNA with a CRISPR kit, or using a sauna delivered to your home? How about a microchip or electrical stimulator?
What could go wrong?
I'm not the neo-police, making citizen's arrests every time someone introduces a new plumbing gadget or extrapolates from animal research on resveratrol or catechins that we should drink more red wine or eat more chocolate. As a scientist who's spent her career asking, "Can we get better?" I've come to view bio-hacking as misguided, profit-driven, and counterproductive to its followers' goals.
We're creatures of nature. Despite all the new gadgets and bio-hacks, we still use Roman plumbing technology, and the best way to stay fit, sharp, and happy is to follow a recipe passed down since the beginning of time. Bacteria, plants, and all natural beings are rhythmic, with alternating periods of high activity and dormancy, whether measured in seconds, hours, days, or seasons. Nature repeats successful patterns.
During the Upstate, every cell in your body is naturally primed and pumped full of glycogen and ATP (your cells' energy currencies), as well as cortisol, which supports your muscles, heart, metabolism, cognitive prowess, emotional regulation, and general "get 'er done" attitude. This big energy release depletes your batteries and requires the Downstate, when your subsystems recharge at the cellular level.
Downstates are when you give your heart a break from pumping nutrient-rich blood through your body; when you give your metabolism a break from inflammation, oxidative stress, and sympathetic arousal caused by eating fast food — or just eating too fast; or when you give your mind a chance to wander, think bigger thoughts, and come up with new creative solutions. When you're responding to notifications, emails, and fires, you can't relax.
Downstates aren't just for consistently recharging your battery. By spending time in the Downstate, your body and brain get extra energy and nutrients, allowing you to grow smarter, faster, stronger, and more self-regulated. This state supports half-marathon training, exam prep, and mediation. As we age, spending more time in the Downstate is key to mental and physical health, well-being, and longevity.
When you prioritize energy-demanding activities during Upstate periods and energy-replenishing activities during Downstate periods, all your subsystems, including cardiovascular, metabolic, muscular, cognitive, and emotional, hum along at their optimal settings. When you synchronize the Upstates and Downstates of these individual rhythms, their functioning improves. A hard workout causes autonomic stress, which triggers Downstate recovery.
By choosing the right timing and type of exercise during the day, you can ensure a deeper recovery and greater readiness for the next workout by working with your natural rhythms and strengthening your autonomic and sleep Downstates.
Morning cardio workouts increase deep sleep compared to afternoon workouts. Timing and type of meals determine when your sleep hormone melatonin is released, ushering in sleep.
Rhythm isn't a hack. It's not a way to cheat the system or the boss. Nature has honed its optimization wisdom over trillions of days and nights. Stop looking for quick fixes. You're a whole system made of smaller subsystems that must work together to function well. No one pill or subsystem will make it all work. Understanding and coordinating your rhythms is free, easy, and only benefits you.
Dr. Sara C. Mednick is a cognitive neuroscientist at UC Irvine and author of The Power of the Downstate (HachetteGO)
Bob Service
3 years ago
Did volcanic 'glasses' play a role in igniting early life?
Quenched lava may have aided in the formation of long RNA strands required by primitive life.
It took a long time for life to emerge. Microbes were present 3.7 billion years ago, just a few hundred million years after the 4.5-billion-year-old Earth had cooled enough to sustain biochemistry, according to fossils, and many scientists believe RNA was the genetic material for these first species. RNA, while not as complicated as DNA, would be difficult to forge into the lengthy strands required to transmit genetic information, raising the question of how it may have originated spontaneously.
Researchers may now have a solution. They demonstrate how basaltic glasses assist individual RNA letters, also known as nucleoside triphosphates, join into strands up to 200 letters long in lab studies. The glasses are formed when lava is quenched in air or water, or when melted rock generated by asteroid strikes cools rapidly, and they would have been plentiful in the early Earth's fire and brimstone.
The outcome has caused a schism among top origin-of-life scholars. "This appears to be a great story that finally explains how nucleoside triphosphates react with each other to create RNA strands," says Thomas Carell, a scientist at Munich's Ludwig Maximilians University. However, Harvard University's Jack Szostak, an RNA expert, says he won't believe the results until the study team thoroughly describes the RNA strands.
Researchers interested in the origins of life like the idea of a primordial "RNA universe" since the molecule can perform two different functions that are essential for life. It's made up of four chemical letters, just like DNA, and can carry genetic information. RNA, like proteins, can catalyze chemical reactions that are necessary for life.
However, RNA can cause headaches. No one has yet discovered a set of plausible primordial conditions that would cause hundreds of RNA letters—each of which is a complicated molecule—to join together into strands long enough to support the intricate chemistry required to kick-start evolution.
Basaltic glasses may have played a role, according to Stephen Mojzsis, a geologist at the University of Colorado, Boulder. They're high in metals like magnesium and iron, which help to trigger a variety of chemical reactions. "Basaltic glass was omnipresent on Earth at the time," he adds.
He provided the Foundation for Applied Molecular Evolution samples of five different basalt glasses. Each sample was ground into a fine powder, sanitized, and combined with a solution of nucleoside triphosphates by molecular biologist Elisa Biondi and her colleagues. The RNA letters were unable to link up without the presence of glass powder. However, when the molecules were mixed with the glass particles, they formed long strands of hundreds of letters, according to the researchers, who published their findings in Astrobiology this week. There was no need for heat or light. Biondi explains, "All we had to do was wait." After only a day, little RNA strands produced, yet the strands continued to grow for months. Jan Paek, a molecular biologist at Firebird Biomolecular Sciences, says, "The beauty of this approach is its simplicity." "Mix the components together, wait a few days, and look for RNA."
Nonetheless, the findings pose a slew of problems. One of the questions is how nucleoside triphosphates came to be in the first place. Recent study by Biondi's colleague Steven Benner suggests that the same basaltic glasses may have aided in the creation and stabilization of individual RNA letters.
The form of the lengthy RNA strands, according to Szostak, is a significant challenge. Enzymes in modern cells ensure that most RNAs form long linear chains. RNA letters, on the other hand, can bind in complicated branching sequences. Szostak wants the researchers to reveal what kind of RNA was produced by the basaltic glasses. "It irritates me that the authors made an intriguing initial finding but then chose to follow the hype rather than the research," Szostak says.
Biondi acknowledges that her team's experiment almost probably results in some RNA branching. She does acknowledge, however, that some branched RNAs are seen in species today, and that analogous structures may have existed before the origin of life. Other studies carried out by the study also confirmed the presence of lengthy strands with connections, indicating that they are most likely linear. "It's a healthy argument," says Dieter Braun, a Ludwig Maximilian University origin-of-life chemist. "It will set off the next series of tests."
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Stephen Moore
3 years ago
Web 2 + Web 3 = Web 5.
Monkey jpegs and shitcoins have tarnished Web3's reputation. Let’s move on.
Web3 was called "the internet's future."
Well, 'crypto bros' shouted about it loudly.
As quickly as it arrived to be the next internet, it appears to be dead. It's had scandals, turbulence, and crashes galore:
Web 3.0's cryptocurrencies have crashed. Bitcoin's all-time high was $66,935. This month, Ethereum fell from $2130 to $1117. Six months ago, the cryptocurrency market peaked at $3 trillion. Worst is likely ahead.
Gas fees make even the simplest Web3 blockchain transactions unsustainable.
Terra, Luna, and other dollar pegs collapsed, hurting crypto markets. Celsius, a crypto lender backed by VCs and Canada's second-largest pension fund, and Binance, a crypto marketplace, have withheld money and coins. They're near collapse.
NFT sales are falling rapidly and losing public interest.
Web3 has few real-world uses, like most crypto/blockchain technologies. Web3's image has been tarnished by monkey profile pictures and shitcoins while failing to become decentralized (the whole concept is controlled by VCs).
The damage seems irreparable, leaving Web3 in the gutter.
Step forward our new saviour — Web5
Fear not though, as hero awaits to drag us out of the Web3 hellscape. Jack Dorsey revealed his plan to save the internet quickly.
Dorsey has long criticized Web3, believing that VC capital and silicon valley insiders have created a centralized platform. In a tweet that upset believers and VCs (he was promptly blocked by Marc Andreessen), Dorsey argued, "You don't own "Web3." VCs and LPs do. Their incentives prevent it. It's a centralized organization with a new name.
Dorsey announced Web5 on June 10 in a very Elon-like manner. Block's TBD unit will work on the project (formerly Square).
Web5's pitch is that users will control their own data and identity. Bitcoin-based. Sound familiar? The presentation pack's official definition emphasizes decentralization. Web5 is a decentralized web platform that enables developers to write decentralized web apps using decentralized identifiers, verifiable credentials, and decentralized web nodes, returning ownership and control over identity and data to individuals.
Web5 would be permission-less, open, and token-less. What that means for Earth is anyone's guess. Identity. Ownership. Blockchains. Bitcoin. Different.
Web4 appears to have been skipped, forever destined to wish it could have shown the world what it could have been. (It was probably crap.) As this iteration combines Web2 and Web3, simple math and common sense add up to 5. Or something.
Dorsey and his team have had this idea simmering for a while. Daniel Buchner, a member of Block's Decentralized Identity team, said, "We're finishing up Web5's technical components."
Web5 could be the project that decentralizes the internet. It must be useful to users and convince everyone to drop the countless Web3 projects, products, services, coins, blockchains, and websites being developed as I write this.
Web5 may be too late for Dorsey and the incoming flood of creators.
Web6 is planned!
The next months and years will be hectic and less stable than the transition from Web 1.0 to Web 2.0.
Web1 was around 1991-2004.
Web2 ran from 2004 to 2021. (though the Web3 term was first used in 2014, it only really gained traction years later.)
Web3 lasted a year.
Web4 is dead.
Silicon Valley billionaires are turning it into a startup-style race, each disrupting the next iteration until they crack it. Or destroy it completely.
Web5 won't last either.
Leonardo Castorina
3 years ago
How to Use Obsidian to Boost Research Productivity
Tools for managing your PhD projects, reading lists, notes, and inspiration.
As a researcher, you have to know everything. But knowledge is useless if it cannot be accessed quickly. An easy-to-use method of archiving information makes taking notes effortless and enjoyable.
As a PhD student in Artificial Intelligence, I use Obsidian (https://obsidian.md) to manage my knowledge.
The article has three parts:
- What is a note, how to organize notes, tags, folders, and links? This section is tool-agnostic, so you can use most of these ideas with any note-taking app.
- Instructions for using Obsidian, managing notes, reading lists, and useful plugins. This section demonstrates how I use Obsidian, my preferred knowledge management tool.
- Workflows: How to use Zotero to take notes from papers, manage multiple projects' notes, create MOCs with Dataview, and more. This section explains how to use Obsidian to solve common scientific problems and manage/maintain your knowledge effectively.
This list is not perfect or complete, but it is my current solution to problems I've encountered during my PhD. Please leave additional comments or contact me if you have any feedback. I'll try to update this article.
Throughout the article, I'll refer to your digital library as your "Obsidian Vault" or "Zettelkasten".
Other useful resources are listed at the end of the article.
1. Philosophy: Taking and organizing notes
Carl Sagan: “To make an apple pie from scratch, you must first create the universe.”
Before diving into Obsidian, let's establish a Personal Knowledge Management System and a Zettelkasten. You can skip to Section 2 if you already know these terms.
Niklas Luhmann, a prolific sociologist who wrote 400 papers and 70 books, inspired this section and much of Zettelkasten. Zettelkasten means “slip box” (or library in this article). His Zettlekasten had around 90000 physical notes, which can be found here.
There are now many tools available to help with this process. Obsidian's website has a good introduction section: https://publish.obsidian.md/hub/
Notes
We'll start with "What is a note?" Although it may seem trivial, the answer depends on the topic or your note-taking style. The idea is that a note is as “atomic” (i.e. You should read the note and get the idea right away.
The resolution of your notes depends on their detail. Deep Learning, for example, could be a general description of Neural Networks, with a few notes on the various architectures (eg. Recurrent Neural Networks, Convolutional Neural Networks etc..).
Limiting length and detail is a good rule of thumb. If you need more detail in a specific section of this note, break it up into smaller notes. Deep Learning now has three notes:
- Deep Learning
- Recurrent Neural Networks
- Convolutional Neural Networks
Repeat this step as needed until you achieve the desired granularity. You might want to put these notes in a “Neural Networks” folder because they are all about the same thing. But there's a better way:
#Tags and [[Links]] over /Folders/
The main issue with folders is that they are not flexible and assume that all notes in the folder belong to a single category. This makes it difficult to make connections between topics.
Deep Learning has been used to predict protein structure (AlphaFold) and classify images (ImageNet). Imagine a folder structure like this:
- /Proteins/
- Protein Folding
- /Deep Learning/
- /Proteins/
Your notes about Protein Folding and Convolutional Neural Networks will be separate, and you won't be able to find them in the same folder.
This can be solved in several ways. The most common one is to use tags rather than folders. A note can be grouped with multiple topics this way. Obsidian tags can also be nested (have subtags).
You can also link two notes together. You can build your “Knowledge Graph” in Obsidian and other note-taking apps like Obsidian.
My Knowledge Graph. Green: Biology, Red: Machine Learning, Yellow: Autoencoders, Blue: Graphs, Brown: Tags.
My Knowledge Graph and the note “Backrpropagation” and its links.
Backpropagation note and all its links
Why use Folders?
Folders help organize your vault as it grows. The main suggestion is to have few folders that "weakly" collect groups of notes or better yet, notes from different sources.
Among my Zettelkasten folders are:
My Zettelkasten's 5 folders
They usually gather data from various sources:
MOC: Map of Contents for the Zettelkasten.
Projects: Contains one note for each side-project of my PhD where I log my progress and ideas. Notes are linked to these.
Bio and ML: These two are the main content of my Zettelkasten and could theoretically be combined.
Papers: All my scientific paper notes go here. A bibliography links the notes. Zotero .bib file
Books: I make a note for each book I read, which I then split into multiple notes.
Keeping images separate from other files can help keep your main folders clean.
I will elaborate on these in the Workflow Section.
My general recommendation is to use tags and links instead of folders.
Maps of Content (MOC)
Making Tables of Contents is a good solution (MOCs).
These are notes that "signposts" your Zettelkasten library, directing you to the right type of notes. It can link to other notes based on common tags. This is usually done with a title, then your notes related to that title. As an example:
An example of a Machine Learning MOC generated with Dataview.
As shown above, my Machine Learning MOC begins with the basics. Then it's on to Variational Auto-Encoders. Not only does this save time, but it also saves scrolling through the tag search section.
So I keep MOCs at the top of my library so I can quickly find information and see my library. These MOCs are generated automatically using an Obsidian Plugin called Dataview (https://github.com/blacksmithgu/obsidian-dataview).
Ideally, MOCs could be expanded to include more information about the notes, their status, and what's left to do. In the absence of this, Dataview does a fantastic job at creating a good structure for your notes.
In the absence of this, Dataview does a fantastic job at creating a good structure for your notes.
2. Tools: Knowing Obsidian
Obsidian is my preferred tool because it is free, all notes are stored in Markdown format, and each panel can be dragged and dropped. You can get it here: https://obsidian.md/
Obsidian interface.
Obsidian is highly customizable, so here is my preferred interface:
The theme is customized from https://github.com/colineckert/obsidian-things
Alternatively, each panel can be collapsed, moved, or removed as desired. To open a panel later, click on the vertical "..." (bottom left of the note panel).
My interface is organized as follows:
How my Obsidian Interface is organized.
Folders/Search:
This is where I keep all relevant folders. I usually use the MOC note to navigate, but sometimes I use the search button to find a note.
Tags:
I use nested tags and look into each one to find specific notes to link.
cMenu:
Easy-to-use menu plugin cMenu (https://github.com/chetachiezikeuzor/cMenu-Plugin)
Global Graph:
The global graph shows all your notes (linked and unlinked). Linked notes will appear closer together. Zoom in to read each note's title. It's a bit overwhelming at first, but as your library grows, you get used to the positions and start thinking of new connections between notes.
Local Graph:
Your current note will be shown in relation to other linked notes in your library. When needed, you can quickly jump to another link and back to the current note.
Links:
Finally, an outline panel and the plugin Obsidian Power Search (https://github.com/aviral-batra/obsidian-power-search) allow me to search my vault by highlighting text.
Start using the tool and worry about panel positioning later. I encourage you to find the best use-case for your library.
Plugins
An additional benefit of using Obsidian is the large plugin library. I use several (Calendar, Citations, Dataview, Templater, Admonition):
Obsidian Calendar Plugin: https://github.com/liamcain
It organizes your notes on a calendar. This is ideal for meeting notes or keeping a journal.
Calendar addon from hans/obsidian-citation-plugin
Obsidian Citation Plugin: https://github.com/hans/
Allows you to cite papers from a.bib file. You can also customize your notes (eg. Title, Authors, Abstract etc..)
Plugin citation from hans/obsidian-citation-plugin
Obsidian Dataview: https://github.com/blacksmithgu/
A powerful plugin that allows you to query your library as a database and generate content automatically. See the MOC section for an example.
Allows you to create notes with specific templates like dates, tags, and headings.
Templater. Obsidian Admonition: https://github.com/valentine195/obsidian-admonition
Blocks allow you to organize your notes.
Plugin warning. Obsidian Admonition (valentine195)
There are many more, but this list should get you started.
3. Workflows: Cool stuff
Here are a few of my workflows for using obsidian for scientific research. This is a list of resources I've found useful for my use-cases. I'll outline and describe them briefly so you can skim them quickly.
3.1 Using Templates to Structure Notes
3.2 Free Note Syncing (Laptop, Phone, Tablet)
3.3 Zotero/Mendeley/JabRef -> Obsidian — Managing Reading Lists
3.4 Projects and Lab Books
3.5 Private Encrypted Diary
3.1 Using Templates to Structure Notes
Plugins: Templater and Dataview (optional).
To take effective notes, you must first make adding new notes as easy as possible. Templates can save you time and give your notes a consistent structure. As an example:
An example of a note using a template.
### [[YOUR MOC]]
# Note Title of your note
**Tags**::
**Links**::
The top line links to your knowledge base's Map of Content (MOC) (see previous sections). After the title, I add tags (and a link between the note and the tag) and links to related notes.
To quickly identify all notes that need to be expanded, I add the tag “#todo”. In the “TODO:” section, I list the tasks within the note.
The rest are notes on the topic.
Templater can help you create these templates. For new books, I use the following template:
### [[Books MOC]]
# Title
**Author**::
**Date::
**Tags::
**Links::
A book template example.
Using a simple query, I can hook Dataview to it.
dataview
table author as Author, date as “Date Finished”, tags as “Tags”, grade as “Grade”
from “4. Books”
SORT grade DESCENDING
using Dataview to query templates.
3.2 Free Note Syncing (Laptop, Phone, Tablet)
No plugins used.
One of my favorite features of Obsidian is the library's self-contained and portable format. Your folder contains everything (plugins included).
Ordinary folders and documents are available as well. There is also a “.obsidian” folder. This contains all your plugins and settings, so you can use it on other devices.
So you can use Google Drive, iCloud, or Dropbox for free as long as you sync your folder (note: your folder should be in your Cloud Folder).
For my iOS and macOS work, I prefer iCloud. You can also use the paid service Obsidian Sync.
3.3 Obsidian — Managing Reading Lists and Notes in Zotero/Mendeley/JabRef
Plugins: Quotes (required).
3.3 Zotero/Mendeley/JabRef -> Obsidian — Taking Notes and Managing Reading Lists of Scientific Papers
My preferred reference manager is Zotero, but this workflow should work with any reference manager that produces a .bib file. This file is exported to my cloud folder so I can access it from any platform.
My Zotero library is tagged as follows:
My reference manager's tags
For readings, I usually search for the tags “!!!” and “To-Read” and select a paper. Annotate the paper next (either on PDF using GoodNotes or on physical paper).
Then I make a paper page using a template in the Citations plugin settings:
An example of my citations template.
Create a new note, open the command list with CMD/CTRL + P, and find the Citations “Insert literature note content in the current pane” to see this lovely view.
Citation generated by the article https://doi.org/10.1101/2022.01.24.22269144
You can then convert your notes to digital. I found that transcribing helped me retain information better.
3.4 Projects and Lab Books
Plugins: Tweaker (required).
PhD students offering advice on thesis writing are common (read as regret). I started asking them what they would have done differently or earlier.
“Deep stuff Leo,” one person said. So my main issue is basic organization, losing track of my tasks and the reasons for them.
As a result, I'd go on other experiments that didn't make sense, and have to reverse engineer my logic for thesis writing. - PhD student now wise Postdoc
Time management requires planning. Keeping track of multiple projects and lab books is difficult during a PhD. How I deal with it:
- One folder for all my projects
- One file for each project
I use a template to create each project
### [[Projects MOC]]
# <% tp.file.title %>
**Tags**::
**Links**::
**URL**::
**Project Description**::## Notes:
### <% tp.file.last_modified_date(“dddd Do MMMM YYYY”) %>
#### Done:
#### TODO:
#### Notes
You can insert a template into a new note with CMD + P and looking for the Templater option.
I then keep adding new days with another template:
### <% tp.file.last_modified_date("dddd Do MMMM YYYY") %>
#### Done:
#### TODO:
#### Notes:
This way you can keep adding days to your project and update with reasonings and things you still have to do and have done. An example below:
Example of project note with timestamped notes.
3.5 Private Encrypted Diary
This is one of my favorite Obsidian uses.
Mini Diary's interface has long frustrated me. After the author archived the project, I looked for a replacement. I had two demands:
- It had to be private, and nobody had to be able to read the entries.
- Cloud syncing was required for editing on multiple devices.
Then I learned about encrypting the Obsidian folder. Then decrypt and open the folder with Obsidian. Sync the folder as usual.
Use CryptoMator (https://cryptomator.org/). Create an encrypted folder in Cryptomator for your Obsidian vault, set a password, and let it do the rest.
If you need a step-by-step video guide, here it is:
Conclusion
So, I hope this was helpful!
In the first section of the article, we discussed notes and note-taking techniques. We discussed when to use tags and links over folders and when to break up larger notes.
Then we learned about Obsidian, its interface, and some useful plugins like Citations for citing papers and Templater for creating note templates.
Finally, we discussed workflows and how to use Zotero to take notes from scientific papers, as well as managing Lab Books and Private Encrypted Diaries.
Thanks for reading and commenting :)
Read original post here
Dmitrii Eliuseev
2 years ago
Creating Images on Your Local PC Using Stable Diffusion AI
Deep learning-based generative art is being researched. As usual, self-learning is better. Some models, like OpenAI's DALL-E 2, require registration and can only be used online, but others can be used locally, which is usually more enjoyable for curious users. I'll demonstrate the Stable Diffusion model's operation on a standard PC.
Let’s get started.
What It Does
Stable Diffusion uses numerous components:
A generative model trained to produce images is called a diffusion model. The model is incrementally improving the starting data, which is only random noise. The model has an image, and while it is being trained, the reversed process is being used to add noise to the image. Being able to reverse this procedure and create images from noise is where the true magic is (more details and samples can be found in the paper).
An internal compressed representation of a latent diffusion model, which may be altered to produce the desired images, is used (more details can be found in the paper). The capacity to fine-tune the generation process is essential because producing pictures at random is not very attractive (as we can see, for instance, in Generative Adversarial Networks).
A neural network model called CLIP (Contrastive Language-Image Pre-training) is used to translate natural language prompts into vector representations. This model, which was trained on 400,000,000 image-text pairs, enables the transformation of a text prompt into a latent space for the diffusion model in the scenario of stable diffusion (more details in that paper).
This figure shows all data flow:
The weights file size for Stable Diffusion model v1 is 4 GB and v2 is 5 GB, making the model quite huge. The v1 model was trained on 256x256 and 512x512 LAION-5B pictures on a 4,000 GPU cluster using over 150.000 NVIDIA A100 GPU hours. The open-source pre-trained model is helpful for us. And we will.
Install
Before utilizing the Python sources for Stable Diffusion v1 on GitHub, we must install Miniconda (assuming Git and Python are already installed):
wget https://repo.anaconda.com/miniconda/Miniconda3-py39_4.12.0-Linux-x86_64.sh
chmod +x Miniconda3-py39_4.12.0-Linux-x86_64.sh
./Miniconda3-py39_4.12.0-Linux-x86_64.sh
conda update -n base -c defaults condaInstall the source and prepare the environment:
git clone https://github.com/CompVis/stable-diffusion
cd stable-diffusion
conda env create -f environment.yaml
conda activate ldm
pip3 install transformers --upgradeDownload the pre-trained model weights next. HiggingFace has the newest checkpoint sd-v14.ckpt (a download is free but registration is required). Put the file in the project folder and have fun:
python3 scripts/txt2img.py --prompt "hello world" --plms --ckpt sd-v1-4.ckpt --skip_grid --n_samples 1Almost. The installation is complete for happy users of current GPUs with 12 GB or more VRAM. RuntimeError: CUDA out of memory will occur otherwise. Two solutions exist.
Running the optimized version
Try optimizing first. After cloning the repository and enabling the environment (as previously), we can run the command:
python3 optimizedSD/optimized_txt2img.py --prompt "hello world" --ckpt sd-v1-4.ckpt --skip_grid --n_samples 1Stable Diffusion worked on my visual card with 8 GB RAM (alas, I did not behave well enough to get NVIDIA A100 for Christmas, so 8 GB GPU is the maximum I have;).
Running Stable Diffusion without GPU
If the GPU does not have enough RAM or is not CUDA-compatible, running the code on a CPU will be 20x slower but better than nothing. This unauthorized CPU-only branch from GitHub is easiest to obtain. We may easily edit the source code to use the latest version. It's strange that a pull request for that was made six months ago and still hasn't been approved, as the changes are simple. Readers can finish in 5 minutes:
Replace if attr.device!= torch.device(cuda) with if attr.device!= torch.device(cuda) and torch.cuda.is available at line 20 of ldm/models/diffusion/ddim.py ().
Replace if attr.device!= torch.device(cuda) with if attr.device!= torch.device(cuda) and torch.cuda.is available in line 20 of ldm/models/diffusion/plms.py ().
Replace device=cuda in lines 38, 55, 83, and 142 of ldm/modules/encoders/modules.py with device=cuda if torch.cuda.is available(), otherwise cpu.
Replace model.cuda() in scripts/txt2img.py line 28 and scripts/img2img.py line 43 with if torch.cuda.is available(): model.cuda ().
Run the script again.
Testing
Test the model. Text-to-image is the first choice. Test the command line example again:
python3 scripts/txt2img.py --prompt "hello world" --plms --ckpt sd-v1-4.ckpt --skip_grid --n_samples 1The slow generation takes 10 seconds on a GPU and 10 minutes on a CPU. Final image:
Hello world is dull and abstract. Try a brush-wielding hamster. Why? Because we can, and it's not as insane as Napoleon's cat. Another image:
Generating an image from a text prompt and another image is interesting. I made this picture in two minutes using the image editor (sorry, drawing wasn't my strong suit):
I can create an image from this drawing:
python3 scripts/img2img.py --prompt "A bird is sitting on a tree branch" --ckpt sd-v1-4.ckpt --init-img bird.png --strength 0.8It was far better than my initial drawing:
I hope readers understand and experiment.
Stable Diffusion UI
Developers love the command line, but regular users may struggle. Stable Diffusion UI projects simplify image generation and installation. Simple usage:
Unpack the ZIP after downloading it from https://github.com/cmdr2/stable-diffusion-ui/releases. Linux and Windows are compatible with Stable Diffusion UI (sorry for Mac users, but those machines are not well-suitable for heavy machine learning tasks anyway;).
Start the script.
Done. The web browser UI makes configuring various Stable Diffusion features (upscaling, filtering, etc.) easy:
V2.1 of Stable Diffusion
I noticed the notification about releasing version 2.1 while writing this essay, and it was intriguing to test it. First, compare version 2 to version 1:
alternative text encoding. The Contrastive LanguageImage Pre-training (CLIP) deep learning model, which was trained on a significant number of text-image pairs, is used in Stable Diffusion 1. The open-source CLIP implementation used in Stable Diffusion 2 is called OpenCLIP. It is difficult to determine whether there have been any technical advancements or if legal concerns were the main focus. However, because the training datasets for the two text encoders were different, the output results from V1 and V2 will differ for the identical text prompts.
a new depth model that may be used to the output of image-to-image generation.
a revolutionary upscaling technique that can quadruple the resolution of an image.
Generally higher resolution Stable Diffusion 2 has the ability to produce both 512x512 and 768x768 pictures.
The Hugging Face website offers a free online demo of Stable Diffusion 2.1 for code testing. The process is the same as for version 1.4. Download a fresh version and activate the environment:
conda deactivate
conda env remove -n ldm # Use this if version 1 was previously installed
git clone https://github.com/Stability-AI/stablediffusion
cd stablediffusion
conda env create -f environment.yaml
conda activate ldmHugging Face offers a new weights ckpt file.
The Out of memory error prevented me from running this version on my 8 GB GPU. Version 2.1 fails on CPUs with the slow conv2d cpu not implemented for Half error (according to this GitHub issue, the CPU support for this algorithm and data type will not be added). The model can be modified from half to full precision (float16 instead of float32), however it doesn't make sense since v1 runs up to 10 minutes on the CPU and v2.1 should be much slower. The online demo results are visible. The same hamster painting with a brush prompt yielded this result:
It looks different from v1, but it functions and has a higher resolution.
The superresolution.py script can run the 4x Stable Diffusion upscaler locally (the x4-upscaler-ema.ckpt weights file should be in the same folder):
python3 scripts/gradio/superresolution.py configs/stable-diffusion/x4-upscaling.yaml x4-upscaler-ema.ckptThis code allows the web browser UI to select the image to upscale:
The copy-paste strategy may explain why the upscaler needs a text prompt (and the Hugging Face code snippet does not have any text input as well). I got a GPU out of memory error again, although CUDA can be disabled like v1. However, processing an image for more than two hours is unlikely:
Stable Diffusion Limitations
When we use the model, it's fun to see what it can and can't do. Generative models produce abstract visuals but not photorealistic ones. This fundamentally limits The generative neural network was trained on text and image pairs, but humans have a lot of background knowledge about the world. The neural network model knows nothing. If someone asks me to draw a Chinese text, I can draw something that looks like Chinese but is actually gibberish because I never learnt it. Generative AI does too! Humans can learn new languages, but the Stable Diffusion AI model includes only language and image decoder brain components. For instance, the Stable Diffusion model will pull NO WAR banner-bearers like this:
V1:
V2.1:
The shot shows text, although the model never learned to read or write. The model's string tokenizer automatically converts letters to lowercase before generating the image, so typing NO WAR banner or no war banner is the same.
I can also ask the model to draw a gorgeous woman:
V1:
V2.1:
The first image is gorgeous but physically incorrect. A second one is better, although it has an Uncanny valley feel. BTW, v2 has a lifehack to add a negative prompt and define what we don't want on the image. Readers might try adding horrible anatomy to the gorgeous woman request.
If we ask for a cartoon attractive woman, the results are nice, but accuracy doesn't matter:
V1:
V2.1:
Another example: I ordered a model to sketch a mouse, which looks beautiful but has too many legs, ears, and fingers:
V1:
V2.1: improved but not perfect.
V1 produces a fun cartoon flying mouse if I want something more abstract:
I tried multiple times with V2.1 but only received this:
The image is OK, but the first version is closer to the request.
Stable Diffusion struggles to draw letters, fingers, etc. However, abstract images yield interesting outcomes. A rural landscape with a modern metropolis in the background turned out well:
V1:
V2.1:
Generative models help make paintings too (at least, abstract ones). I searched Google Image Search for modern art painting to see works by real artists, and this was the first image:
I typed "abstract oil painting of people dancing" and got this:
V1:
V2.1:
It's a different style, but I don't think the AI-generated graphics are worse than the human-drawn ones.
The AI model cannot think like humans. It thinks nothing. A stable diffusion model is a billion-parameter matrix trained on millions of text-image pairs. I input "robot is creating a picture with a pen" to create an image for this post. Humans understand requests immediately. I tried Stable Diffusion multiple times and got this:
This great artwork has a pen, robot, and sketch, however it was not asked. Maybe it was because the tokenizer deleted is and a words from a statement, but I tried other requests such robot painting picture with pen without success. It's harder to prompt a model than a person.
I hope Stable Diffusion's general effects are evident. Despite its limitations, it can produce beautiful photographs in some settings. Readers who want to use Stable Diffusion results should be warned. Source code examination demonstrates that Stable Diffusion images feature a concealed watermark (text StableDiffusionV1 and SDV2) encoded using the invisible-watermark Python package. It's not a secret, because the official Stable Diffusion repository's test watermark.py file contains a decoding snippet. The put watermark line in the txt2img.py source code can be removed if desired. I didn't discover this watermark on photographs made by the online Hugging Face demo. Maybe I did something incorrectly (but maybe they are just not using the txt2img script on their backend at all).
Conclusion
The Stable Diffusion model was fascinating. As I mentioned before, trying something yourself is always better than taking someone else's word, so I encourage readers to do the same (including this article as well;).
Is Generative AI a game-changer? My humble experience tells me:
I think that place has a lot of potential. For designers and artists, generative AI can be a truly useful and innovative tool. Unfortunately, it can also pose a threat to some of them since if users can enter a text field to obtain a picture or a website logo in a matter of clicks, why would they pay more to a different party? Is it possible right now? unquestionably not yet. Images still have a very poor quality and are erroneous in minute details. And after viewing the image of the stunning woman above, models and fashion photographers may also unwind because it is highly unlikely that AI will replace them in the upcoming years.
Today, generative AI is still in its infancy. Even 768x768 images are considered to be of a high resolution when using neural networks, which are computationally highly expensive. There isn't an AI model that can generate high-resolution photographs natively without upscaling or other methods, at least not as of the time this article was written, but it will happen eventually.
It is still a challenge to accurately represent knowledge in neural networks (information like how many legs a cat has or the year Napoleon was born). Consequently, AI models struggle to create photorealistic photos, at least where little details are important (on the other side, when I searched Google for modern art paintings, the results are often even worse;).
When compared to the carefully chosen images from official web pages or YouTube reviews, the average output quality of a Stable Diffusion generation process is actually less attractive because to its high degree of randomness. When using the same technique on their own, consumers will theoretically only view those images as 1% of the results.
Anyway, it's exciting to witness this area's advancement, especially because the project is open source. Google's Imagen and DALL-E 2 can also produce remarkable findings. It will be interesting to see how they progress.